Requirements

knowledge

PILMBC 103: https://pilm-bioinformatics.github.io/pilmbc103-remote-storage-and-computing/
What is RNAseq: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2949280/

Software

Docker: https://docs.docker.com/v17.12/install/
nexflow: In the terminal do this:

java -version This has to return a version > 8 or >1.8

curl -s https://get.nextflow.io | bash

./nextflow run hello

Agenda

1:30-1:55 Introduction to vim hands-on: modify files in the terminal (mandatory if you don’t know this)
2:00-2:25 Best practices for RNAseq analysis lecture
2:30-3:50 Running an example in the local computer hands-on
3:00-3:30 Running an example in OpenMind cluster hands-on: you need to be part of the cluster, contact your representative:
- millerlab : Jefferson Roy
- surlab: Ming Hu
- tsailab: Lorena Pantano

You are welcome to stay during the whole session even if you don’t want/can’t to follow the hands-on materials.

Goal

Best practices on choosing the right tool
How to process FASTQ files from RNAseq experiments
Run a test data analysis in your computer or/and the Open Mind cluster

Angels

If you see you can help others during the workshop, please do, it will improve the dynamic.

Contributors

Happy to accept corrections at: https://github.com/pilm-bioinformatics/pilmbc211-rnaseq-i